!--------------------------------------------------------------------------------------------------!
!   CP2K: A general program to perform molecular dynamics simulations                              !
!   Copyright 2000-2025 CP2K developers group <https://cp2k.org>                                   !
!                                                                                                  !
!   SPDX-License-Identifier: GPL-2.0-or-later                                                      !
!--------------------------------------------------------------------------------------------------!

! **************************************************************************************************
!> \par History
!>      - taken out of input_cp2k_motion
!> \author Ole Schuett
! **************************************************************************************************

MODULE input_cp2k_md
   USE bibliography,                    ONLY: &
        Evans1983, Guidon2008, Kantorovich2008, Kantorovich2008a, Kuhne2007, Minary2003, &
        Rengaraj2020, Ricci2003, Tuckerman1992, VandeVondele2002, West2006
   USE cp_output_handling,              ONLY: add_last_numeric,&
                                              cp_print_key_section_create,&
                                              debug_print_level,&
                                              high_print_level,&
                                              low_print_level,&
                                              medium_print_level
   USE cp_units,                        ONLY: cp_unit_to_cp2k
   USE input_constants,                 ONLY: &
        isokin_ensemble, langevin_ensemble, md_init_default, md_init_vib, npe_f_ensemble, &
        npe_i_ensemble, nph_ensemble, nph_uniaxial_damped_ensemble, nph_uniaxial_ensemble, &
        npt_f_ensemble, npt_i_ensemble, npt_ia_ensemble, nve_ensemble, nvt_adiabatic_ensemble, &
        nvt_ensemble, reftraj_ensemble
   USE input_cp2k_barostats,            ONLY: create_barostat_section
   USE input_cp2k_thermostats,          ONLY: create_region_section,&
                                              create_thermo_fast_section,&
                                              create_thermo_slow_section,&
                                              create_thermostat_section
   USE input_keyword_types,             ONLY: keyword_create,&
                                              keyword_release,&
                                              keyword_type
   USE input_section_types,             ONLY: section_add_keyword,&
                                              section_add_subsection,&
                                              section_create,&
                                              section_release,&
                                              section_type
   USE input_val_types,                 ONLY: integer_t,&
                                              lchar_t,&
                                              real_t
   USE kinds,                           ONLY: dp
   USE reftraj_types,                   ONLY: REFTRAJ_EVAL_ENERGY,&
                                              REFTRAJ_EVAL_ENERGY_FORCES,&
                                              REFTRAJ_EVAL_NONE
   USE string_utilities,                ONLY: s2a
#include "../base/base_uses.f90"

   IMPLICIT NONE
   PRIVATE

   LOGICAL, PRIVATE, PARAMETER :: debug_this_module = .TRUE.
   CHARACTER(len=*), PARAMETER, PRIVATE :: moduleN = 'input_cp2k_md'

   PUBLIC :: create_md_section

CONTAINS

! **************************************************************************************************
!> \brief ...
!> \param section will contain the md section
!> \author fawzi
! **************************************************************************************************
   SUBROUTINE create_md_section(section)
      TYPE(section_type), POINTER                        :: section

      TYPE(keyword_type), POINTER                        :: keyword
      TYPE(section_type), POINTER                        :: subsection

      CPASSERT(.NOT. ASSOCIATED(section))
      CALL section_create(section, __LOCATION__, name="MD", &
                          description="This section defines the whole set of parameters needed perform an MD run.", &
                          n_keywords=13, n_subsections=6, repeats=.FALSE.)

      NULLIFY (keyword, subsection)
      CALL keyword_create(keyword, __LOCATION__, name="ensemble", &
                          description="The ensemble/integrator that you want to use for MD propagation", &
                          usage="ensemble nve", &
                          default_i_val=nve_ensemble, &
                          enum_c_vals=s2a("NVE", "NVT", "NPT_I", "NPT_F", "MSST", "MSST_DAMPED", &
                                          "HYDROSTATICSHOCK", "ISOKIN", "REFTRAJ", "LANGEVIN", "NPE_F", &
                                          "NPE_I", "NVT_ADIABATIC", "NPT_IA"), &
                          enum_desc=s2a("constant energy (microcanonical)", &
                                        "constant temperature and volume (canonical)", &
                                        "constant temperature and pressure using an isotropic cell", &
                                        "constant temperature and pressure using a flexible cell", &
                                        "simulate steady shock (uniaxial)", &
                                        "simulate steady shock (uniaxial) with extra viscosity", &
                                        "simulate steady shock with hydrostatic pressure", &
                                        "constant kinetic energy", &
                                        "reading frames from a file called reftraj.xyz (e.g. for property calculation)", &
                                        "langevin dynamics (constant temperature)", &
                                        "constant pressure ensemble (no thermostat)", &
                                        "constant pressure ensemble using an isotropic cell (no thermostat)", &
                                        "adiabatic dynamics in constant temperature and volume ensemble (CAFES)", &
                                        "NPT_I ensemble with frozen atoms in absolute coordinate"), &
                          citations=[Evans1983, VandeVondele2002, Minary2003], &
                          enum_i_vals=[nve_ensemble, nvt_ensemble, npt_i_ensemble, npt_f_ensemble, &
                                       nph_uniaxial_ensemble, nph_uniaxial_damped_ensemble, nph_ensemble, isokin_ensemble, &
                                       reftraj_ensemble, langevin_ensemble, npe_f_ensemble, npe_i_ensemble, &
                                       nvt_adiabatic_ensemble, npt_ia_ensemble])
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

      CALL keyword_create(keyword, __LOCATION__, name="steps", &
                          description="The number of MD steps to perform, counting from step_start_val. ", &
                          usage="steps 100", default_i_val=3)
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

      CALL keyword_create(keyword, __LOCATION__, name="max_steps", &
                          description="The number of MD steps to perform, counting from step 1", &
                          usage="max_steps 100", default_i_val=1000000000)
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

      CALL keyword_create(keyword, __LOCATION__, name="timestep", &
                          description="The length of an integration step (in case RESPA the large TIMESTEP)", &
                          usage="timestep 1.0", default_r_val=cp_unit_to_cp2k(value=0.5_dp, unit_str="fs"), &
                          unit_str="fs")
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

      CALL keyword_create(keyword, __LOCATION__, name="step_start_val", &
                          description="The starting step value for the MD", usage="step_start_val <integer>", &
                          default_i_val=0)
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

      CALL keyword_create(keyword, __LOCATION__, name="time_start_val", &
                          description="The starting timer value for the MD", &
                          usage="time_start_val <real>", default_r_val=cp_unit_to_cp2k(value=0.0_dp, unit_str="fs"), &
                          unit_str="fs")
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

      CALL keyword_create(keyword, __LOCATION__, name="econs_start_val", &
                          description="The starting  value of the conserved quantity", &
                          usage="econs_start_val <real>", default_r_val=0.0_dp, &
                          unit_str="hartree")
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

      CALL keyword_create(keyword, __LOCATION__, name="temperature", &
                          description="The temperature in K used to initialize "// &
                          "the velocities with init and pos restart, and in the NPT/NVT simulations", &
                          usage="temperature 325.0", default_r_val=cp_unit_to_cp2k(value=300.0_dp, unit_str="K"), &
                          unit_str="K")
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

      CALL keyword_create(keyword, __LOCATION__, name="temp_tol", &
                          variants=s2a("temp_to", "temperature_tolerance"), &
                          description="The maximum accepted deviation of the (global) temperature "// &
                          "from the desired target temperature before a rescaling of the velocites "// &
                          "is performed. If it is 0 no rescaling is performed. NOTE: This keyword is "// &
                          "obsolescent; Using a CSVR thermostat with a short timeconstant is "// &
                          "recommended as a better alternative.", &
                          usage="temp_tol 0.0", default_r_val=0.0_dp, unit_str='K')
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

      CALL keyword_create(keyword, __LOCATION__, name="temp_kind", &
                          description="Compute the temperature per each kind separately", &
                          usage="temp_kind LOGICAL", &
                          default_l_val=.FALSE., lone_keyword_l_val=.TRUE.)
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

      CALL keyword_create(keyword, __LOCATION__, name="scale_temp_kind", &
                          description="When necessary rescale the temperature per each kind separately", &
                          usage="scale_temp_kind LOGICAL", &
                          default_l_val=.FALSE., lone_keyword_l_val=.TRUE.)
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

      CALL keyword_create(keyword, __LOCATION__, name="comvel_tol", &
                          description="The maximum accepted velocity of the center of mass. "// &
                          "With Shell-Model, comvel may drift if MD%THERMOSTAT%REGION /= GLOBAL ", &
                          usage="comvel_tol 0.1", type_of_var=real_t, n_var=1, unit_str="bohr*au_t^-1")
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

      CALL keyword_create(keyword, __LOCATION__, name="angvel_tol", &
                          description="The maximum accepted angular velocity. This option is ignored "// &
                          "when the system is periodic. Removes the components of the velocities that "// &
                          "project on the external rotational degrees of freedom.", &
                          usage="angvel_tol 0.1", type_of_var=real_t, n_var=1, unit_str="bohr*au_t^-1")
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

      CALL keyword_create(keyword, __LOCATION__, name="angvel_zero", &
                          description="Set the initial angular velocity to zero. This option is ignored "// &
                          "when the system is periodic or when initial velocities are defined. Technically, "// &
                          "the part of the random initial velocities that projects on the external "// &
                          "rotational degrees of freedom is subtracted.", &
                          usage="angvel_zero LOGICAL", &
                          default_l_val=.FALSE., lone_keyword_l_val=.TRUE.)
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

      CALL keyword_create(keyword, __LOCATION__, name="ANNEALING", &
                          description="Specifies the rescaling factor for annealing velocities. "// &
                          "Automatically enables the annealing procedure. This scheme works only for ensembles "// &
                          "that do not have thermostats on particles.", &
                          usage="annealing <REAL>", default_r_val=1.0_dp)
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

      CALL keyword_create(keyword, __LOCATION__, name="ANNEALING_CELL", &
                          description="Specifies the rescaling factor for annealing velocities of the CELL "// &
                          "Automatically enables the annealing procedure for the CELL. This scheme works only "// &
                          "for ensambles that do not have thermostat on CELLS velocities.", &
                          usage="ANNEALING_CELL <REAL>", default_r_val=1.0_dp)
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

      CALL keyword_create(keyword, __LOCATION__, name="TEMPERATURE_ANNEALING", &
                          description="Specifies the rescaling factor for the external temperature. "// &
                          "This scheme works only for the Langevin ensemble.", &
                          usage="TEMPERATURE_ANNEALING <REAL>", default_r_val=1.0_dp)
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

      CALL keyword_create(keyword, __LOCATION__, name="DISPLACEMENT_TOL", &
                          description="This keyword sets a maximum atomic displacement "// &
                          "in each Cartesian direction. "// &
                          "The maximum velocity is evaluated and if it is too large to remain "// &
                          "within the assigned limit, the time step is rescaled accordingly, "// &
                          "and the first half step of the velocity verlet is repeated.", &
                          usage="DISPLACEMENT_TOL <REAL>", default_r_val=100.0_dp, &
                          unit_str='angstrom')
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

      CALL keyword_create(keyword, __LOCATION__, name="INITIALIZATION_METHOD", &
                          description="This keyword selects which method to use to initialize MD. "// &
                          "If velecities are not set explicitly, DEFAULT optioin will assign "// &
                          "random velocities and then scale according to TEMPERATURE; VIBRATIONAL "// &
                          "option will then use previously calculated vibrational modes to "// &
                          "initialise both the atomic positions and velocities so that the "// &
                          "starting point for MD is as close to canonical ensemble as possible, "// &
                          "without the need for lengthy equilibration steps. See PRL 96, 115504 "// &
                          "(2006). The user input atomic positions in this case are expected to "// &
                          "be already geometry optimised. Further options for VIBRATIONAL mode "// &
                          "is can be set in INITIAL_VIBRATION subsection. If unspecified, then "// &
                          "the DEFAULT mode will be used.", &
                          usage="INITIALIZATION_METHOD DEFAULT", &
                          default_i_val=md_init_default, &
                          enum_c_vals=s2a("DEFAULT", "VIBRATIONAL"), &
                          enum_desc=s2a("Assign random velocities and then scale according to "// &
                                        "TEMPERATURE", &
                                        "Initialise positions and velocities to give canonical ensemble "// &
                                        "with TEMPERATURE, using the method described in PRL 96, 115504 (2006)"), &
                          enum_i_vals=[md_init_default, md_init_vib])
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

      CALL create_langevin_section(subsection)
      CALL section_add_subsection(section, subsection)
      CALL section_release(subsection)

      CALL create_msst_section(subsection)
      CALL section_add_subsection(section, subsection)
      CALL section_release(subsection)

      CALL create_barostat_section(subsection)
      CALL section_add_subsection(section, subsection)
      CALL section_release(subsection)

      CALL create_thermostat_section(subsection)
      CALL section_add_subsection(section, subsection)
      CALL section_release(subsection)

      CALL create_respa_section(subsection)
      CALL section_add_subsection(section, subsection)
      CALL section_release(subsection)

      CALL create_shell_section(subsection)
      CALL section_add_subsection(section, subsection)
      CALL section_release(subsection)

      CALL create_adiabatic_section(subsection)
      CALL section_add_subsection(section, subsection)
      CALL section_release(subsection)

      CALL create_softening_section(subsection)
      CALL section_add_subsection(section, subsection)
      CALL section_release(subsection)

      CALL create_reftraj_section(subsection)
      CALL section_add_subsection(section, subsection)
      CALL section_release(subsection)

      CALL create_avgs_section(subsection)
      CALL section_add_subsection(section, subsection)
      CALL section_release(subsection)

      CALL create_thermal_region_section(subsection)
      CALL section_add_subsection(section, subsection)
      CALL section_release(subsection)

      CALL create_md_print_section(subsection)
      CALL section_add_subsection(section, subsection)
      CALL section_release(subsection)

      CALL create_cascade_section(subsection)
      CALL section_add_subsection(section, subsection)
      CALL section_release(subsection)

      CALL create_vib_init_section(subsection)
      CALL section_add_subsection(section, subsection)
      CALL section_release(subsection)

   END SUBROUTINE create_md_section

! **************************************************************************************************
!> \brief Defines LANGEVIN section
!> \param section ...
!> \author teo
! **************************************************************************************************
   SUBROUTINE create_langevin_section(section)
      TYPE(section_type), POINTER                        :: section

      TYPE(keyword_type), POINTER                        :: keyword

      CPASSERT(.NOT. ASSOCIATED(section))
      CALL section_create(section, __LOCATION__, name="Langevin", &
                          description="Controls the set of parameters to run a Langevin MD. "// &
                          "The integrator used follows that given in the article by Ricci et al. "// &
                          "The user can define regions in the system where the atoms inside "// &
                          "undergoes Langevin MD, while those outside the regions undergoes "// &
                          "NVE Born Oppenheimer MD. To define the regions, the user should "// &
                          "use THERMAL_REGION subsection of MOTION%MD. ", &
                          citations=[Ricci2003, Kuhne2007, Rengaraj2020], &
                          n_keywords=0, n_subsections=1, repeats=.FALSE.)
      NULLIFY (keyword)

      CALL keyword_create(keyword, __LOCATION__, name="gamma", &
                          description="Gamma parameter for the Langevin dynamics (LD)", &
                          usage="gamma 0.001", &
                          default_r_val=0.0_dp, unit_str='fs^-1')
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

      CALL keyword_create(keyword, __LOCATION__, name="Noisy_Gamma", &
                          variants=["NoisyGamma"], &
                          description="Imaginary Langevin Friction term for LD with noisy forces.", &
                          citations=[Kuhne2007], &
                          usage="Noisy_Gamma 4.0E-5", default_r_val=0.0_dp, unit_str='fs^-1')
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

      CALL keyword_create(keyword, __LOCATION__, name="Shadow_Gamma", &
                          variants=["ShadowGamma"], &
                          description="Shadow Langevin Friction term for LD with noisy forces in order to adjust Noisy_Gamma.", &
                          citations=[Rengaraj2020], &
                          usage="Shadow_Gamma 0.001", default_r_val=0.0_dp, unit_str='fs^-1')
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)
   END SUBROUTINE create_langevin_section

! **************************************************************************************************
!> \brief Defines print section for MD
!> \param section ...
!> \author teo
! **************************************************************************************************
   SUBROUTINE create_md_print_section(section)
      TYPE(section_type), POINTER                        :: section

      TYPE(keyword_type), POINTER                        :: keyword
      TYPE(section_type), POINTER                        :: print_key

      CPASSERT(.NOT. ASSOCIATED(section))
      CALL section_create(section, __LOCATION__, name="print", &
                          description="Controls the printing properties during an MD run", &
                          n_keywords=0, n_subsections=1, repeats=.FALSE.)
      NULLIFY (print_key, keyword)

      CALL keyword_create(keyword, __LOCATION__, name="FORCE_LAST", &
                          description="Print the output and restart file if walltime is reached or "// &
                          "if an external EXIT command is given. It still requires the keyword LAST "// &
                          "to be present for the specific print key (in case the last step should not "// &
                          "match with the print_key iteration number).", &
                          usage="FORCE_LAST LOGICAL", &
                          default_l_val=.FALSE., lone_keyword_l_val=.TRUE.)
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

      CALL cp_print_key_section_create(print_key, __LOCATION__, "ENERGY", &
                                       description="Controls the output the ener file", &
                                       print_level=low_print_level, common_iter_levels=1, &
                                       filename="")
      CALL section_add_subsection(section, print_key)
      CALL section_release(print_key)

      CALL cp_print_key_section_create(print_key, __LOCATION__, "SHELL_ENERGY", &
                                       description="Controls the output of the shell-energy file (only if shell-model)", &
                                       print_level=medium_print_level, common_iter_levels=1, &
                                       filename="")
      CALL section_add_subsection(section, print_key)
      CALL section_release(print_key)

      CALL cp_print_key_section_create(print_key, __LOCATION__, "TEMP_KIND", &
                                       description="Controls the output of the temperature"// &
                                       " computed separately for each kind", &
                                       print_level=high_print_level, common_iter_levels=1, &
                                       filename="")
      CALL section_add_subsection(section, print_key)
      CALL section_release(print_key)

      CALL cp_print_key_section_create(print_key, __LOCATION__, "TEMP_SHELL_KIND", &
                                       description="Controls the output of the temperature of the"// &
                                       " shell-core motion computed separately for each kind", &
                                       print_level=high_print_level, common_iter_levels=1, &
                                       filename="")
      CALL section_add_subsection(section, print_key)
      CALL section_release(print_key)

      CALL cp_print_key_section_create(print_key, __LOCATION__, "CENTER_OF_MASS", &
                                       description="Controls the printing of COM velocity during an MD", &
                                       print_level=medium_print_level, common_iter_levels=1, &
                                       filename="__STD_OUT__")
      CALL section_add_subsection(section, print_key)
      CALL section_release(print_key)

      CALL cp_print_key_section_create(print_key, __LOCATION__, "COEFFICIENTS", &
                                       description="Controls the printing of coefficients during an MD run.", &
                                       print_level=medium_print_level, common_iter_levels=1, &
                                       filename="")
      CALL section_add_subsection(section, print_key)
      CALL section_release(print_key)

      CALL cp_print_key_section_create(print_key, __LOCATION__, "ROTATIONAL_INFO", &
                                       description="Controls the printing basic info during the calculation of the "// &
                                       "translational/rotational degrees of freedom.", print_level=low_print_level, &
                                       add_last=add_last_numeric, filename="__STD_OUT__")
      CALL keyword_create(keyword, __LOCATION__, name="COORDINATES", &
                          description="Prints atomic coordinates in the standard orientation. "// &
                          "Coordinates are not affected during the calculation.", &
                          default_l_val=.FALSE., lone_keyword_l_val=.TRUE.)
      CALL section_add_keyword(print_key, keyword)
      CALL keyword_release(keyword)
      CALL section_add_subsection(section, print_key)
      CALL section_release(print_key)

      CALL cp_print_key_section_create(print_key, __LOCATION__, "PROGRAM_RUN_INFO", &
                                       description="Controls the printing of basic and summary information during the"// &
                                       " Molecular Dynamics", &
                                       print_level=low_print_level, add_last=add_last_numeric, filename="__STD_OUT__")
      CALL section_add_subsection(section, print_key)
      CALL section_release(print_key)
   END SUBROUTINE create_md_print_section

! **************************************************************************************************
!> \brief Defines parameters for RESPA integration scheme
!> \param section will contain the coeff section
!> \author teo
! **************************************************************************************************
   SUBROUTINE create_respa_section(section)
      TYPE(section_type), POINTER                        :: section

      TYPE(keyword_type), POINTER                        :: keyword

      CPASSERT(.NOT. ASSOCIATED(section))

      CALL section_create(section, __LOCATION__, name="RESPA", &
                          description="Multiple timestep integration based on RESPA (implemented for NVE only)."// &
                          " RESPA exploits multiple force_eval."// &
                          " In this case the order of the force_eval maps"// &
                          " the order of the respa shells from the slowest to the fastest force evaluation."// &
                          " If force_evals share the same subsys, it's enough then to specify the"// &
                          " subsys in the force_eval corresponding at the first index in the multiple_force_eval list."// &
                          " Can be used to speedup classical and ab initio MD simulations.", &
                          n_keywords=1, n_subsections=0, repeats=.FALSE., &
                          citations=[Tuckerman1992, Guidon2008])

      NULLIFY (keyword)
      CALL keyword_create(keyword, __LOCATION__, name="FREQUENCY", &
                          description="The number of reference MD steps between two RESPA corrections.", &
                          usage="FREQUENCY <INTEGER>", default_i_val=5)
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

   END SUBROUTINE create_respa_section

! **************************************************************************************************
!> \brief Defines parameters for REFTRAJ analysis
!> \param section will contain the coeff section
!> \author teo
! **************************************************************************************************
   SUBROUTINE create_reftraj_section(section)
      TYPE(section_type), POINTER                        :: section

      TYPE(keyword_type), POINTER                        :: keyword
      TYPE(section_type), POINTER                        :: print_key, subsection

      CPASSERT(.NOT. ASSOCIATED(section))

      CALL section_create(section, __LOCATION__, name="REFTRAJ", &
                          description="Loads an external trajectory file and performs analysis on the"// &
                          " loaded snapshots.", &
                          n_keywords=1, n_subsections=1, repeats=.FALSE.)

      NULLIFY (keyword, print_key, subsection)

      CALL keyword_create(keyword, __LOCATION__, name="TRAJ_FILE_NAME", &
                          description="Specify the filename where the trajectory is stored. "// &
                          "If you built your own trajectory file make sure it has the trajectory format. "// &
                          'In particular, each structure has to be enumerated using " i = ..."', &
                          repeats=.FALSE., &
                          usage="TRAJ_FILE_NAME <CHARACTER>", default_lc_val="reftraj.xyz")
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

      CALL keyword_create(keyword, __LOCATION__, name="CELL_FILE_NAME", &
                          description="Specify the filename where the cell is stored "// &
                          "(for trajectories generated within variable cell ensembles).", repeats=.FALSE., &
                          usage="CELL_FILE_NAME <CHARACTER>", default_lc_val="reftraj.cell")
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

      CALL keyword_create( &
         keyword, __LOCATION__, name="VARIABLE_VOLUME", &
         description="Enables the possibility to read a CELL file with information on the CELL size during the MD.", &
         repeats=.FALSE., default_l_val=.FALSE., lone_keyword_l_val=.TRUE.)
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

      CALL keyword_create(keyword, __LOCATION__, name="FIRST_SNAPSHOT", &
                          description="Index of the snapshot stored in the trajectory file "// &
                          "from which to start a REFTRAJ run", &
                          repeats=.FALSE., usage="FIRST_SNAPSHOT <INTEGER>", default_i_val=1)
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

      CALL keyword_create(keyword, __LOCATION__, name="LAST_SNAPSHOT", &
                          description="Index of the last snapshot stored in the trajectory file "// &
                          "that is read along a REFTRAJ run. Must be specified as default is 0. "// &
                          "Must be specified exactly as LAST_SNAPSHOT = FIRST_SNAPSHOT + STRIDE*(number of strides) "// &
                          "to avoid an error 'Unexpected EOF'. Note that STRIDE*(number of strides) "// &
                          "is simply the number of steps between the first to last snapshot.", &
                          repeats=.FALSE., usage="LAST_SNAPSHOT", default_i_val=0)
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

      CALL keyword_create(keyword, __LOCATION__, name="STRIDE", &
                          description=" Stride in number of snapshot for the  reftraj analysis", &
                          repeats=.FALSE., usage="STRIDE", default_i_val=1)
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

      CALL keyword_create(keyword, __LOCATION__, name="EVAL", &
                          description="Selects the properties to evaluate for each retrieved snapshot during a REFTRAJ run", &
                          default_i_val=REFTRAJ_EVAL_NONE, &
                          enum_i_vals=[REFTRAJ_EVAL_NONE, REFTRAJ_EVAL_ENERGY, REFTRAJ_EVAL_ENERGY_FORCES], &
                          enum_c_vals=s2a("NONE", "ENERGY", "ENERGY_FORCES"), &
                          enum_desc=s2a("Evaluate nothing", "Evaluate only the energy", "Evaluate energy and forces"))
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

      CALL keyword_create(keyword, __LOCATION__, name="eval_energy_forces", &
                          description="Evaluate energy and forces for each retrieved snapshot during a REFTRAJ run", &
                          repeats=.FALSE., default_l_val=.FALSE., lone_keyword_l_val=.TRUE., &
                          deprecation_notice="Please use MOTION / MD / REFTRAJ / EVAL instead.")
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

      CALL keyword_create(keyword, __LOCATION__, name="eval_forces", &
                          description="Evaluate the forces for each retrieved snapshot during a REFTRAJ run", &
                          repeats=.FALSE., default_l_val=.FALSE., lone_keyword_l_val=.TRUE., &
                          deprecation_notice="Please use MOTION / MD / REFTRAJ / EVAL instead.")
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

      CALL create_msd_section(subsection)
      CALL section_add_subsection(section, subsection)
      CALL section_release(subsection)

      CALL section_create(subsection, __LOCATION__, name="print", &
                          description="The section that controls the output of a reftraj run", &
                          n_keywords=1, n_subsections=0, repeats=.FALSE.)

      NULLIFY (print_key)
      CALL cp_print_key_section_create(print_key, __LOCATION__, "msd_kind", &
                                       description="Controls the output of msd per kind", &
                                       print_level=low_print_level, common_iter_levels=1, &
                                       filename="")
      CALL section_add_subsection(subsection, print_key)
      CALL section_release(print_key)

      CALL cp_print_key_section_create(print_key, __LOCATION__, "msd_molecule", &
                                       description="Controls the output of msd per molecule kind", &
                                       print_level=low_print_level, common_iter_levels=1, &
                                       filename="")
      CALL section_add_subsection(subsection, print_key)
      CALL section_release(print_key)

      CALL cp_print_key_section_create(print_key, __LOCATION__, "displaced_atom", &
                                       description="Controls the output of index and dislacement of "// &
                                       "atoms that moved away from the initial position of more than a "// &
                                       "given distance (see msd%disp_tol)", &
                                       print_level=low_print_level, common_iter_levels=1, &
                                       filename="")
      CALL section_add_subsection(subsection, print_key)
      CALL section_release(print_key)

      CALL section_add_subsection(section, subsection)
      CALL section_release(subsection)

   END SUBROUTINE create_reftraj_section

! **************************************************************************************************
!> \brief Defines parameters for MSD calculation along a REFTRAJ analysis
!> \param section will contain the coeff section
!> \author MI
! **************************************************************************************************
   SUBROUTINE create_msd_section(section)
      TYPE(section_type), POINTER                        :: section

      TYPE(keyword_type), POINTER                        :: keyword
      TYPE(section_type), POINTER                        :: subsection

      CPASSERT(.NOT. ASSOCIATED(section))

      CALL section_create(section, __LOCATION__, name="MSD", &
                          description="Loads an external trajectory file and performs analysis on the"// &
                          " loaded snapshots.", &
                          n_keywords=3, n_subsections=0, repeats=.FALSE.)

      NULLIFY (keyword, subsection)

      CALL keyword_create(keyword, __LOCATION__, name="_SECTION_PARAMETERS_", &
                          description="controls the activation of core-level spectroscopy simulations", &
                          usage="&MSD T", &
                          default_l_val=.FALSE., &
                          lone_keyword_l_val=.TRUE.)
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

      CALL keyword_create(keyword, __LOCATION__, name="REF0_FILENAME", &
                          description="Specify the filename where the initial reference configuration is stored.", &
                          repeats=.FALSE., usage="REF0_FILENAME <CHARACTER>", default_lc_val="")
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

      CALL keyword_create(keyword, __LOCATION__, name="MSD_PER_KIND", &
                          description="Set up the calculation of the MSD for each atomic kind", &
                          usage="MSD_PER_KIND <LOGICAL>", repeats=.FALSE., &
                          default_l_val=.FALSE., lone_keyword_l_val=.TRUE.)
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

      CALL keyword_create(keyword, __LOCATION__, name="MSD_PER_MOLKIND", &
                          description="Set up the calculation of the MSD for each molecule kind. "// &
                          "The position of the center of mass of the molecule is considered.", &
                          usage="MSD_PER_MOLKIND <LOGICAL>", repeats=.FALSE., &
                          default_l_val=.FALSE., lone_keyword_l_val=.TRUE.)
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

      CALL keyword_create(keyword, __LOCATION__, name="MSD_PER_REGION", &
                          description="Set up the calculation of the MSD for each defined region.", &
                          usage="MSD_PER_REGION <LOGICAL>", repeats=.FALSE., &
                          default_l_val=.FALSE., lone_keyword_l_val=.TRUE.)
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

      CALL create_region_section(subsection, "MSD calculation")
      CALL section_add_subsection(section, subsection)
      CALL section_release(subsection)

      CALL keyword_create(keyword, __LOCATION__, name="DISPLACED_ATOM", &
                          description="Identify the atoms that moved from their initial "// &
                          "position of a distance larger than a given tolerance (see msd%displacement_tol).", &
                          usage="DISPLACED_ATOM <LOGICAL>", repeats=.FALSE., &
                          default_l_val=.FALSE., lone_keyword_l_val=.TRUE.)
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

      CALL keyword_create(keyword, __LOCATION__, name="displacement_tol", &
                          description="Lower limit to define displaced atoms", &
                          usage="DISPLACEMENT_TOL real", &
                          default_r_val=0._dp, n_var=1, unit_str='bohr')
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

   END SUBROUTINE create_msd_section

! **************************************************************************************************
!> \brief ...
!> \param section will contain the coeff section
!> \author teo
! **************************************************************************************************
   SUBROUTINE create_msst_section(section)
      TYPE(section_type), POINTER                        :: section

      TYPE(keyword_type), POINTER                        :: keyword

      CPASSERT(.NOT. ASSOCIATED(section))

      CALL section_create(section, __LOCATION__, name="msst", &
                          description="Parameters for Multi-Scale Shock Technique (MSST) "// &
                          "which simulate the effect of a steady planar shock on a unit cell. "// &
                          "Reed et. al. Physical Review Letters 90, 235503 (2003).", &
                          n_keywords=1, n_subsections=0, repeats=.FALSE.)

      NULLIFY (keyword)
      CALL keyword_create(keyword, __LOCATION__, name="PRESSURE", &
                          description="Initial pressure", &
                          usage="PRESSURE real", &
                          default_r_val=0._dp, n_var=1, unit_str='bar')
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

      CALL keyword_create(keyword, __LOCATION__, name="ENERGY", &
                          description="Initial energy", &
                          usage="ENERGY real", &
                          default_r_val=0._dp, n_var=1, unit_str='hartree')
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

      CALL keyword_create(keyword, __LOCATION__, name="VOLUME", &
                          description="Initial volume", &
                          usage="VOLUME real", &
                          default_r_val=0._dp, n_var=1, unit_str='angstrom^3')
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

      CALL keyword_create(keyword, __LOCATION__, name="CMASS", &
                          description="Effective cell mass", &
                          usage="CMASS real", &
                          default_r_val=0._dp, n_var=1, unit_str='au_m')
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

      CALL keyword_create(keyword, __LOCATION__, name="VSHOCK", variants=["V_SHOCK"], &
                          description="Velocity shock", &
                          usage="VSHOCK real", &
                          default_r_val=0._dp, n_var=1, unit_str='m/s')
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

      CALL keyword_create(keyword, __LOCATION__, name="GAMMA", &
                          description="Damping coefficient for cell volume", &
                          usage="GAMMA real", &
                          unit_str='fs^-1', &
                          default_r_val=0.0_dp)
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

   END SUBROUTINE create_msst_section

! **************************************************************************************************
!> \brief section will contain some parameters for the shells dynamics
!> \param section ...
! **************************************************************************************************
   SUBROUTINE create_shell_section(section)
      TYPE(section_type), POINTER                        :: section

      TYPE(keyword_type), POINTER                        :: keyword
      TYPE(section_type), POINTER                        :: thermo_section

      CPASSERT(.NOT. ASSOCIATED(section))

      CALL section_create(section, __LOCATION__, name="shell", &
                          description="Parameters of shell model in adiabatic dynamics.", &
                          n_keywords=4, n_subsections=1, repeats=.FALSE.)

      NULLIFY (keyword, thermo_section)

      CALL keyword_create(keyword, __LOCATION__, name="temperature", &
                          description="Temperature in K used to control "// &
                          "the internal velocities of the core-shell motion ", &
                          usage="temperature 5.0", &
                          default_r_val=cp_unit_to_cp2k(value=0.0_dp, unit_str="K"), &
                          unit_str="K")
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

      CALL keyword_create(keyword, __LOCATION__, name="temp_tol", &
                          description="Maximum accepted temperature deviation"// &
                          " from the expected value, for the internal core-shell motion."// &
                          " If 0, no rescaling is performed", &
                          usage="temp_tol 0.0", default_r_val=0.0_dp, unit_str='K')
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

      CALL keyword_create(keyword, __LOCATION__, name="nose_particle", &
                          description="If nvt or npt, the core and shell velocities are controlled "// &
                          "by the same thermostat used for the particle. This might favour heat exchange "// &
                          "and additional rescaling of the internal core-shell velocity is needed (TEMP_TOL)", &
                          default_l_val=.FALSE., lone_keyword_l_val=.TRUE.)
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

      CALL keyword_create(keyword, __LOCATION__, name="DISPLACEMENT_SHELL_TOL", &
                          description="This keyword sets a maximum variation of the shell"// &
                          " core distance in each Cartesian direction."// &
                          " The maximum internal core-shell velocity is evaluated and"// &
                          " if it is too large to remain"// &
                          " within the assigned limit, the time step is rescaled accordingly,"// &
                          " and the first half step of the velocity verlet is repeated.", &
                          usage="DISPLACEMENT_SHELL_TOL <REAL>", default_r_val=100.0_dp, &
                          unit_str='angstrom')
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

      CALL create_thermostat_section(thermo_section)
      CALL section_add_subsection(section, thermo_section)
      CALL section_release(thermo_section)

   END SUBROUTINE create_shell_section

! **************************************************************************************************
!> \brief section will contain some parameters for the adiabatic dynamics
!> \param section ...
! **************************************************************************************************
   SUBROUTINE create_adiabatic_section(section)
      TYPE(section_type), POINTER                        :: section

      TYPE(keyword_type), POINTER                        :: keyword
      TYPE(section_type), POINTER                        :: thermo_fast_section, thermo_slow_section

      CPASSERT(.NOT. ASSOCIATED(section))

      CALL section_create(section, __LOCATION__, name="ADIABATIC_DYNAMICS", &
                          description="Parameters used in canonical adiabatic free energy sampling (CAFES).", &
                          n_keywords=5, n_subsections=2, repeats=.FALSE., &
                          citations=[VandeVondele2002])

      NULLIFY (keyword, thermo_fast_section, thermo_slow_section)

      CALL keyword_create(keyword, __LOCATION__, name="temp_fast", &
                          description="Temperature in K used to control "// &
                          "the fast degrees of freedom ", &
                          usage="temp_fast 5.0", &
                          default_r_val=cp_unit_to_cp2k(value=0.0_dp, unit_str="K"), &
                          unit_str="K")
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

      CALL keyword_create(keyword, __LOCATION__, name="temp_slow", &
                          description="Temperature in K used to control "// &
                          "the slow degrees of freedom ", &
                          usage="temp_slow 5.0", &
                          default_r_val=cp_unit_to_cp2k(value=0.0_dp, unit_str="K"), &
                          unit_str="K")
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

      CALL keyword_create(keyword, __LOCATION__, name="temp_tol_fast", &
                          description="Maximum accepted temperature deviation"// &
                          " from the expected value, for the fast motion."// &
                          " If 0, no rescaling is performed", &
                          usage="temp_tol_fast 0.0", default_r_val=0.0_dp, unit_str='K')
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

      CALL keyword_create(keyword, __LOCATION__, name="temp_tol_slow", &
                          description="Maximum accepted temperature deviation"// &
                          " from the expected value, for the slow motion."// &
                          " If 0, no rescaling is performed", &
                          usage="temp_tol_slow 0.0", default_r_val=0.0_dp, unit_str='K')
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

      CALL keyword_create(keyword, __LOCATION__, name="n_resp_fast", &
                          description="number of respa steps for fast degrees of freedom", &
                          repeats=.FALSE., default_i_val=1)
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

      CALL create_thermo_fast_section(thermo_fast_section)
      CALL section_add_subsection(section, thermo_fast_section)
      CALL section_release(thermo_fast_section)

      CALL create_thermo_slow_section(thermo_slow_section)
      CALL section_add_subsection(section, thermo_slow_section)
      CALL section_release(thermo_slow_section)

   END SUBROUTINE create_adiabatic_section

! **************************************************************************************************
!> \brief section will contain parameters for the velocity softening
!> \param section ...
!> \author Ole Schuett
! **************************************************************************************************
   SUBROUTINE create_softening_section(section)
      TYPE(section_type), POINTER                        :: section

      TYPE(keyword_type), POINTER                        :: keyword

      CALL section_create(section, __LOCATION__, name="VELOCITY_SOFTENING", &
                          description="A method to initialize the velocities along low-curvature " &
                          //"directions in order to favors MD trajectories to cross rapidly over " &
                          //"small energy barriers into neighboring basins. " &
                          //"In each iteration the forces are calculated at a point y, which " &
                          //"is slightly displaced from the current positions x in the direction " &
                          //"of the original velocities v. The velocities are then updated with " &
                          //"the force component F_t, which is perpendicular to N. " &
                          //"N = v / |v|;  y = x + delta * N;  F_t = F(y) - &lang; F(y) | N &rang; * N; " &
                          //"v' = v + alpha * F_t")

      NULLIFY (keyword)
      CALL keyword_create(keyword, __LOCATION__, name="STEPS", &
                          description="Number of softening iterations performed. " &
                          //"Typical values are around 40 steps.", &
                          default_i_val=0)
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

      CALL keyword_create(keyword, __LOCATION__, name="DELTA", &
                          description="Displacement used to obtain y.", &
                          default_r_val=0.1_dp)
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

      CALL keyword_create(keyword, __LOCATION__, name="ALPHA", &
                          description="Mixing factor used for updating velocities.", &
                          default_r_val=0.15_dp)
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

   END SUBROUTINE create_softening_section

! **************************************************************************************************
!> \brief input section used to define regions with different temperature
!>        initialization and control
!> \param section ...
!> \par History
!>   - Added input for langevin regions in thermal regions section
!>     (2014/02/04, LT)
! **************************************************************************************************
   SUBROUTINE create_thermal_region_section(section)
      TYPE(section_type), POINTER                        :: section

      TYPE(keyword_type), POINTER                        :: keyword
      TYPE(section_type), POINTER                        :: print_key, region_section, subsection

      CPASSERT(.NOT. ASSOCIATED(section))

      CALL section_create(section, __LOCATION__, name="thermal_region", &
                          description="Define regions where different initialization and control "// &
                          "of the temperature is used. When MOTION%MD%ENSEMBLE is set to LANGEVIN, "// &
                          "this section controls if the atoms defined inside and outside the "// &
                          "thermal regions should undergo Langevin MD or NVE Born-Oppenheimer MD. "// &
                          "The theory behind Langevin MD using different regions can be found in "// &
                          "articles by Kantorovitch et al. listed below.", &
                          citations=[Kantorovich2008, Kantorovich2008a], &
                          n_keywords=0, n_subsections=1, repeats=.FALSE.)

      NULLIFY (region_section)
      NULLIFY (keyword, subsection)

      CALL keyword_create(keyword, __LOCATION__, name="force_rescaling", &
                          description="Control the rescaling ot the velocities in all the regions, "// &
                          "according to the temperature assigned to each reagion, when "// &
                          "RESTART_VELOCITY in EXT_RESTART is active.", &
                          default_l_val=.FALSE., lone_keyword_l_val=.TRUE.)
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

      CALL keyword_create(keyword, __LOCATION__, name="do_langevin_default", &
                          description="If ENSEMBLE is set to LANGEVIN, controls whether the "// &
                          "atoms NOT defined in the thermal regions to undergo langevin MD "// &
                          "or not. If not, then the atoms will undergo NVE Born-Oppenheimer MD.", &
                          usage="do_langevin_default .FALSE.", &
                          default_l_val=.FALSE., lone_keyword_l_val=.TRUE.)
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

      CALL section_create(region_section, __LOCATION__, name="DEFINE_REGION", &
                          description="This section provides the possibility to define arbitrary region ", &
                          n_keywords=3, n_subsections=0, repeats=.TRUE.)

      NULLIFY (keyword)
      CALL keyword_create(keyword, __LOCATION__, name="LIST", &
                          description="Specifies a list of atoms belonging to the region.", &
                          usage="LIST {integer} {integer} .. {integer}", &
                          repeats=.TRUE., n_var=-1, type_of_var=integer_t)
      CALL section_add_keyword(region_section, keyword)
      CALL keyword_release(keyword)

      CALL keyword_create(keyword, __LOCATION__, name="temperature", &
                          description="The temperature in K used to initialize the velocities "// &
                          "of the atoms in this region ", &
                          usage="temperature 5.0", &
                          default_r_val=cp_unit_to_cp2k(value=0.0_dp, unit_str="K"), &
                          unit_str="K")
      CALL section_add_keyword(region_section, keyword)
      CALL keyword_release(keyword)

      CALL keyword_create(keyword, __LOCATION__, name="temp_tol", &
                          description="Maximum accepted temperature deviation from the expected "// &
                          "value for this region. If temp_tol=0 no rescaling is performed", &
                          usage="temp_tol 0.0", &
                          default_r_val=0.0_dp, unit_str='K')
      CALL section_add_keyword(region_section, keyword)
      CALL keyword_release(keyword)

      CALL keyword_create(keyword, __LOCATION__, name="do_langevin", &
                          description="When ENSEMBLE is set to LANGEVIN, Controls whether "// &
                          "the atoms in the thermal region should undergo Langevin MD. If "// &
                          "not, then they will undergo NVE Born-Oppenheimer MD.", &
                          usage="do_langevin .TRUE.", &
                          default_l_val=.TRUE., lone_keyword_l_val=.TRUE.)
      CALL section_add_keyword(region_section, keyword)
      CALL keyword_release(keyword)

      CALL keyword_create(keyword, __LOCATION__, name="noisy_gamma_region", &
                          description="Special imaginary Langevin Friction term"// &
                          " for Langevin Dynamics with noisy forces for the atoms in this region."// &
                          " When set, overrides the general value set by NOISY_GAMMA in the MOTION%MD%LANGEVIN section."// &
                          " When unset for a defined region, the general NOISY_GAMMA value applies.", &
                          citations=[Kuhne2007], usage="noisy_gamma_region 4.0E-5", &
                          type_of_var=real_t, &
                          unit_str="fs^-1")
      CALL section_add_keyword(region_section, keyword)
      CALL keyword_release(keyword)

      CALL section_add_subsection(section, region_section)
      CALL section_release(region_section)

      NULLIFY (print_key)
      CALL section_create(subsection, __LOCATION__, name="PRINT", &
                          description="Collects all print_keys for thermal_regions", &
                          n_keywords=1, n_subsections=0, repeats=.FALSE.)

      CALL cp_print_key_section_create(print_key, __LOCATION__, "TEMPERATURE", &
                                       description="Controls output of temperature per region.", &
                                       print_level=high_print_level, common_iter_levels=1, &
                                       filename="")
      CALL section_add_subsection(subsection, print_key)
      CALL section_release(print_key)

      CALL cp_print_key_section_create(print_key, __LOCATION__, "LANGEVIN_REGIONS", &
                                       description="Controls output of information on which atoms "// &
                                       "underwent Langevin MD and which atoms did not.", &
                                       print_level=high_print_level, &
                                       filename="")
      CALL section_add_subsection(subsection, print_key)
      CALL section_release(print_key)

      CALL section_add_subsection(section, subsection)
      CALL section_release(subsection)

   END SUBROUTINE create_thermal_region_section

! **************************************************************************************************
!> \brief   Defines the parameters for the setup of a cascade simulation
!> \param section ...
!> \date    03.02.2012
!> \author  Matthias Krack (MK)
!> \version 1.0
! **************************************************************************************************
   SUBROUTINE create_cascade_section(section)

      TYPE(section_type), POINTER                        :: section

      TYPE(keyword_type), POINTER                        :: keyword
      TYPE(section_type), POINTER                        :: subsection

      NULLIFY (keyword)
      NULLIFY (subsection)
      CPASSERT(.NOT. ASSOCIATED(section))

      CALL section_create(section, __LOCATION__, name="CASCADE", &
                          description="Defines the parameters for the setup of a cascade simulation.", &
                          n_keywords=1, &
                          n_subsections=1, &
                          repeats=.FALSE.)

      CALL keyword_create(keyword, __LOCATION__, &
                          name="_SECTION_PARAMETERS_", &
                          description="Controls the activation of the CASCADE section.", &
                          usage="&CASCADE on", &
                          default_l_val=.FALSE., &
                          lone_keyword_l_val=.TRUE.)
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

      CALL keyword_create(keyword, __LOCATION__, name="ENERGY", &
                          description="Total energy transferred to the system during the cascade event.", &
                          usage="ENERGY 20.0", &
                          default_r_val=0.0_dp, &
                          unit_str="keV")
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

      CALL section_create(subsection, __LOCATION__, name="ATOM_LIST", &
                          description="Defines a list of atoms for which the initial velocities are modified", &
                          n_keywords=1, &
                          n_subsections=0, &
                          repeats=.FALSE.)

      CALL keyword_create(keyword, __LOCATION__, name="_DEFAULT_KEYWORD_", &
                          description="Defines the list of atoms for which the velocities are modified. "// &
                          "Each record consists of the atomic index, the velocity vector, and "// &
                          "a weight to define which fraction of the total energy is assigned "// &
                          "to the current atom: `Atomic_index  v_x  v_y  v_z  Weight`", &
                          usage="{{Integer} {Real} {Real} {Real} {Real}}", &
                          repeats=.TRUE., &
                          type_of_var=lchar_t)
      CALL section_add_keyword(subsection, keyword)
      CALL keyword_release(keyword)

      CALL section_add_subsection(section, subsection)
      CALL section_release(subsection)

   END SUBROUTINE create_cascade_section

! **************************************************************************************************
!> \brief Defines AVERAGES section
!> \param section ...
!> \author teo
! **************************************************************************************************
   SUBROUTINE create_avgs_section(section)
      TYPE(section_type), POINTER                        :: section

      TYPE(keyword_type), POINTER                        :: keyword
      TYPE(section_type), POINTER                        :: print_key, subsection

      CPASSERT(.NOT. ASSOCIATED(section))
      CALL section_create(section, __LOCATION__, name="Averages", &
                          description="Controls the calculation of the averages during an MD run.", &
                          n_keywords=1, n_subsections=1, repeats=.FALSE.)
      NULLIFY (keyword, print_key, subsection)

      CALL keyword_create(keyword, __LOCATION__, name="_SECTION_PARAMETERS_", &
                          description="Controls the calculations of the averages.", &
                          usage="&AVERAGES T", default_l_val=.TRUE., lone_keyword_l_val=.TRUE.)
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

      CALL keyword_create(keyword, __LOCATION__, name="ACQUISITION_START_TIME", &
                          description="Setup up the simulation time when the acquisition process to compute"// &
                          " averages is started.", &
                          usage="ACQUISITION_START_TIME <REAL>", &
                          default_r_val=0.0_dp, unit_str='fs')
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

      CALL keyword_create(keyword, __LOCATION__, name="AVERAGE_COLVAR", &
                          description="Switch for computing the averages of COLVARs.", &
                          usage="AVERAGE_COLVAR <LOGICAL>", default_l_val=.FALSE., &
                          lone_keyword_l_val=.TRUE.)
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

      CALL cp_print_key_section_create(print_key, __LOCATION__, "PRINT_AVERAGES", &
                                       description="Controls the output the averaged quantities", &
                                       print_level=debug_print_level + 1, common_iter_levels=1, &
                                       filename="")
      CALL section_add_subsection(section, print_key)
      CALL section_release(print_key)

      CALL create_avgs_restart_section(subsection)
      CALL section_add_subsection(section, subsection)
      CALL section_release(subsection)
   END SUBROUTINE create_avgs_section

! **************************************************************************************************
!> \brief Defines the AVERAGES RESTART section
!> \param section ...
!> \author teo
! **************************************************************************************************
   SUBROUTINE create_avgs_restart_section(section)
      TYPE(section_type), POINTER                        :: section

      TYPE(keyword_type), POINTER                        :: keyword

      CPASSERT(.NOT. ASSOCIATED(section))
      CALL section_create(section, __LOCATION__, name="RESTART_AVERAGES", &
                          description="Stores information for restarting averages.", &
                          n_keywords=1, n_subsections=1, repeats=.FALSE.)
      NULLIFY (keyword)

      CALL keyword_create(keyword, __LOCATION__, name="ITIMES_START", &
                          description="TIME STEP starting the evaluation of averages", &
                          usage="ITIMES_START <INTEGER>", type_of_var=integer_t, n_var=1)
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

      CALL keyword_create(keyword, __LOCATION__, name="AVECPU", &
                          description="CPU average", usage="AVECPU <REAL>", &
                          type_of_var=real_t, n_var=1)
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

      CALL keyword_create(keyword, __LOCATION__, name="AVEHUGONIOT", &
                          description="HUGONIOT average", usage="AVEHUGONIOT <REAL>", &
                          type_of_var=real_t, n_var=1)
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

      CALL keyword_create(keyword, __LOCATION__, name="AVETEMP_BARO", &
                          description="BAROSTAT TEMPERATURE average", usage="AVETEMP_BARO <REAL>", &
                          type_of_var=real_t, n_var=1)
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

      CALL keyword_create(keyword, __LOCATION__, name="AVEPOT", &
                          description="POTENTIAL ENERGY average", usage="AVEPOT <REAL>", &
                          type_of_var=real_t, n_var=1)
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

      CALL keyword_create(keyword, __LOCATION__, name="AVEKIN", &
                          description="KINETIC ENERGY average", usage="AVEKIN <REAL>", &
                          type_of_var=real_t, n_var=1)
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

      CALL keyword_create(keyword, __LOCATION__, name="AVETEMP", &
                          description="TEMPERATURE average", usage="AVETEMP <REAL>", &
                          type_of_var=real_t, n_var=1)
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

      CALL keyword_create(keyword, __LOCATION__, name="AVEKIN_QM", &
                          description="QM KINETIC ENERGY average in QMMM runs", usage="AVEKIN_QM <REAL>", &
                          type_of_var=real_t, n_var=1)
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

      CALL keyword_create(keyword, __LOCATION__, name="AVETEMP_QM", &
                          description="QM TEMPERATURE average in QMMM runs", usage="AVETEMP_QM <REAL>", &
                          type_of_var=real_t, n_var=1)
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

      CALL keyword_create(keyword, __LOCATION__, name="AVEVOL", &
                          description="VOLUME average", usage="AVEVOL <REAL>", &
                          type_of_var=real_t, n_var=1)
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

      CALL keyword_create(keyword, __LOCATION__, name="AVECELL_A", &
                          description="CELL VECTOR A average", usage="AVECELL_A <REAL>", &
                          type_of_var=real_t, n_var=1)
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

      CALL keyword_create(keyword, __LOCATION__, name="AVECELL_B", &
                          description="CELL VECTOR B average", usage="AVECELL_B <REAL>", &
                          type_of_var=real_t, n_var=1)
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

      CALL keyword_create(keyword, __LOCATION__, name="AVECELL_C", &
                          description="CELL VECTOR C average", usage="AVECELL_C <REAL>", &
                          type_of_var=real_t, n_var=1)
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

      CALL keyword_create(keyword, __LOCATION__, name="AVEALPHA", &
                          description="ALPHA cell angle average", usage="AVEALPHA <REAL>", &
                          type_of_var=real_t, n_var=1)
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

      CALL keyword_create(keyword, __LOCATION__, name="AVEBETA", &
                          description="BETA cell angle average", usage="AVEBETA <REAL>", &
                          type_of_var=real_t, n_var=1)
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

      CALL keyword_create(keyword, __LOCATION__, name="AVEGAMMA", &
                          description="GAMMA cell angle average", usage="AVEGAMMA <REAL>", &
                          type_of_var=real_t, n_var=1)
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

      CALL keyword_create(keyword, __LOCATION__, name="AVE_ECONS", &
                          description="CONSTANT ENERGY average", usage="AVE_ECONS <REAL>", &
                          type_of_var=real_t, n_var=1)
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

      CALL keyword_create(keyword, __LOCATION__, name="AVE_PRESS", &
                          description="PRESSURE average", usage="AVE_PRESS <REAL>", &
                          type_of_var=real_t, n_var=1)
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

      CALL keyword_create(keyword, __LOCATION__, name="AVE_PXX", &
                          description="P_{XX} average", usage="AVE_PXX <REAL>", &
                          type_of_var=real_t, n_var=1)
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

      CALL keyword_create(keyword, __LOCATION__, name="AVE_PV_VIR", &
                          description="PV VIRIAL average", usage="AVE_PV_VIR <REAL> .. <REAL>", &
                          type_of_var=real_t, n_var=9)
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

      CALL keyword_create(keyword, __LOCATION__, name="AVE_PV_TOT", &
                          description="PV TOTAL average", usage="AVE_PV_TOT <REAL> .. <REAL>", &
                          type_of_var=real_t, n_var=9)
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

      CALL keyword_create(keyword, __LOCATION__, name="AVE_PV_KIN", &
                          description="PV KINETIC average", usage="AVE_PV_KIN <REAL> .. <REAL>", &
                          type_of_var=real_t, n_var=9)
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

      CALL keyword_create(keyword, __LOCATION__, name="AVE_PV_CNSTR", &
                          description="PV CONSTRAINTS average", usage="AVE_PV_CNSTR <REAL> .. <REAL>", &
                          type_of_var=real_t, n_var=9)
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

      CALL keyword_create(keyword, __LOCATION__, name="AVE_PV_XC", &
                          description="PV XC average", usage="AVE_PV_XC <REAL> .. <REAL>", &
                          type_of_var=real_t, n_var=9)
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

      CALL keyword_create(keyword, __LOCATION__, name="AVE_PV_FOCK_4C", &
                          description="PV XC average", usage="AVE_PV_FOCK_4C <REAL> .. <REAL>", &
                          type_of_var=real_t, n_var=9)
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

      CALL keyword_create(keyword, __LOCATION__, name="AVE_COLVARS", &
                          description="COLVARS averages", usage="AVE_COLVARS <REAL> .. <REAL>", &
                          type_of_var=real_t, n_var=-1)
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)

      CALL keyword_create(keyword, __LOCATION__, name="AVE_MMATRIX", &
                          description="METRIC TENSOR averages", usage="AVE_MMATRIX <REAL> .. <REAL>", &
                          type_of_var=real_t, n_var=-1)
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)
   END SUBROUTINE create_avgs_restart_section

! **************************************************************************************************
!> \brief Defines the INITIAL_VIBRATION section
!> \param section ...
!> \author Lianheng Tong
! **************************************************************************************************
   SUBROUTINE create_vib_init_section(section)
      TYPE(section_type), POINTER                        :: section

      TYPE(keyword_type), POINTER                        :: keyword

      CPASSERT(.NOT. ASSOCIATED(section))
      CALL section_create(section, __LOCATION__, name="INITIAL_VIBRATION", &
                          description="Controls the set of parameters for MD initialisation "// &
                          "based on vibration analysis data. The starting atomic coordinates "// &
                          "should be based on the relaxed positions obtained from a previous "// &
                          "geometry/cell optimisation calculation, and the vibrational "// &
                          "frequencies and displacements data should be obtained from a "// &
                          "vibrational analysis calculation done based on the relaxed "// &
                          "coordinates. The MD initialisation process expects the user has "// &
                          "performed both geometry optimisation and vibrational analysis "// &
                          "before hand, and won't perform those calculations automatically ", &
                          citations=[West2006], &
                          n_keywords=0, n_subsections=1, repeats=.FALSE.)
      NULLIFY (keyword)
      CALL keyword_create(keyword, __LOCATION__, name="VIB_EIGS_FILE_NAME", &
                          description="The file name of vibrational frequency (eigenvalue) "// &
                          "and displacement (eigenvector) data calculated from the a "// &
                          "vibrational analysis calculation done previously. This file must "// &
                          "be the same unformatted binary file as referred to by "// &
                          "VIBRATIONAL_ANALYSIS%PRINT%CARTESIAN_EIGS keyword. If this keyword "// &
                          "is not explicitly defined by the user, then the default file "// &
                          "name of: <project_name>-<CARTESIAN_EIGS_FILENAME>.eig will be used", &
                          usage="VIB_EIGS_FILE_NAME <FILENAME>", &
                          type_of_var=lchar_t)
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)
      NULLIFY (keyword)
      CALL keyword_create(keyword, __LOCATION__, name="PHASE", &
                          description="Controls the initial ratio of potential and kinetic "// &
                          "contribution to the total energy. The contribution is determined by "// &
                          "COS**2(2*pi*PHASE) for potential energy, and SIN**2(2*pi*PHASE) "// &
                          "for kinetic energy. If PHASE is negative, then for each vibration "// &
                          "mode the phase is determined randomly. Otherwise, PHASE must be "// &
                          "between 0.0 and 1.0 and will be the same for all vibration modes. "// &
                          "If value > 1.0 it will just be treated as 1.0. "// &
                          "For example, setting PHASE = 0.25 would set all modes to "// &
                          "begin with entirely kinetic energy --- in other words, the initial "// &
                          "atomic positions will remain at their optimised location", &
                          default_r_val=-1.0_dp, &
                          usage="PHASE <REAL>")
      CALL section_add_keyword(section, keyword)
      CALL keyword_release(keyword)
   END SUBROUTINE create_vib_init_section

END MODULE input_cp2k_md
